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  • s_#_sorted.txt files

    hello,
    im a NGS newbie and i have some solexa data from their pipeline v1.3. can the s_#_sorted.txt files be used in MAQ and how?. i believe these files contain reads that map to the genome uniquely.

    thank you

  • #2
    You might be better off using filtered reads from the export file since MAQ gives non unique reads a low mapping quality and thus do not contribute to SNP calling. Also even though the documentation states that sorted.txt contains only uniquely aligning reads I have seen cases where a sorted.txt file contains reads which DO map to more than one location.

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    • #3
      unique reads

      oh ok. so im using the s_#_sequence.txt file in MAQ, i presume this is just as good as the export.txt file? im using the 'match' command with default settings and 'assemble' with -q 10. Is this sufficient to get alignments consisting only of unique reads, i.e reads that map to only one position?.

      thanks for your help

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